Strain identifier

BacDive ID: 24261

Type strain: Yes

Species: Herminiimonas contaminans

Strain history: <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; CCUG 53591 <- CCUG

NCBI tax ID(s): 1111140 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 20498

BacDive-ID: 24261

DSM-Number: 28178

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Herminiimonas contaminans DSM 28178 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from contaminant of biopharmaceutical process.

NCBI tax id

  • NCBI tax id: 1111140
  • Matching level: species

strain history

  • @ref: 20498
  • history: <- P. Kämpfer, Justus-Liebig-Universität, Giessen, Germany; CCUG 53591 <- CCUG

doi: 10.13145/bacdive24261.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Oxalobacteraceae
  • genus: Herminiimonas
  • species: Herminiimonas contaminans
  • full scientific name: Herminiimonas contaminans Kämpfer et al. 2013

@ref: 20498

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Oxalobacteraceae

genus: Herminiimonas

species: Herminiimonas contaminans

full scientific name: Herminiimonas contaminans Kämpfer et al. 2013

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30576negative1 µm0.5 µmrod-shapedyes
69480yes95.634
69480negative99.999

pigmentation

  • @ref: 30576
  • production: yes

multimedia

  • @ref: 20498
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28178.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 20498
  • name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/535
  • composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20498positivegrowth28mesophilic
30576positivegrowth04-30
30576positiveoptimum27.5mesophilic
59938positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
30576aerobe
59938aerobe

spore formation

@refspore formationconfidence
30576no
69481no100
69480no100

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3057630089acetate+carbon source
3057624996lactate+carbon source
3057625115malate+carbon source
3057617272propionate+carbon source

enzymes

@refvalueactivityec
30576catalase+1.11.1.6
30576cytochrome oxidase+1.9.3.1
30576urease+3.5.1.5

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    59938C14:00.414
    59938C16:020.116
    59938C10:0 3OH7.511.423
    59938C16:1 ω7c9.915.819
    59938C17:0 CYCLO41.716.888
    59938C18:1 ω7c /12t/9t4.417.824
    59938C19:0 CYCLO ω8c10.718.9
    59938C19:0 ISO0.518.633
    59938Unidentified0.39.985
    59938Unidentified0.916.09
    59938Unidentified0.917.751
    59938Unidentified0.418.962
    59938unknown 18.4451.118.445
    59938unknown 9.1401.49.14
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling date
20498contaminant of biopharmaceutical processSwedenSWEEurope
59938Contaminant,biopharmaceuticalsSwedenSWEEurope2006-10-01

isolation source categories

Cat1Cat2Cat3
#Engineered#Industrial#Engineered product
#Engineered#Laboratory#Contaminant

taxonmaps

  • @ref: 69479
  • File name: preview.99_5056.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_12;96_2343;97_2853;98_3549;99_5056&stattab=map
  • Last taxonomy: Herminiimonas
  • 16S sequence: HE610501
  • Sequence Identity:
  • Total samples: 2485
  • soil counts: 780
  • aquatic counts: 491
  • animal counts: 395
  • plant counts: 819

Safety information

risk assessment

  • @ref: 20498
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20498
  • description: Herminiimonas contaminans partial 16S rRNA gene, type strain CCUG 53591T
  • accession: HE610501
  • length: 1442
  • database: ena
  • NCBI tax ID: 1111140

Genome sequences

  • @ref: 66792
  • description: Herminiimonas contaminans strain Marseille-Q4544
  • accession: 1111140.3
  • assembly level: wgs
  • database: patric
  • NCBI tax ID: 1111140

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes89.706no
flagellatedyes72.802no
gram-positiveno98.206no
anaerobicno98.626no
aerobicyes88.829yes
halophileno95.152no
spore-formingno95.128yes
thermophileno99.428yes
glucose-utilno70.802no
glucose-fermentno91.19no

External links

@ref: 20498

culture collection no.: DSM 28178, CCM 7991, CCUG 53591

straininfo link

  • @ref: 88203
  • straininfo: 303389

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny22447701Herminiimonas contaminans sp. nov., isolated as a contaminant of biopharmaceuticals.Kampfer P, P Glaeser S, Lodders N, Busse HJ, Falsen EInt J Syst Evol Microbiol10.1099/ijs.0.039073-02012Bacterial Typing Techniques, DNA, Bacterial/genetics, *Drug Contamination, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Oxalobacteraceae/*classification/genetics/isolation & purification, *Phylogeny, Polyamines/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysisGenetics
Genetics33602736Draft Genome Sequence of Herminiimonas contaminans Strain CCM 7991(T), a Biopharmaceutical Contaminant.Kangale LJ, Zgheib R, Ghigo E, Raoult D, Fournier PEMicrobiol Resour Announc10.1128/MRA.01432-202021

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
20498Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28178Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28178)
30576Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172690728776041
59938Curators of the CCUGhttps://www.ccug.se/strain?id=53591Culture Collection University of Gothenburg (CCUG) (CCUG 53591)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
88203Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID303389.1